The success of many tissue culture techniques, including organogenesis and somatic embryogenesis depends upon the proper formation of de novo meristems, the function of which affects the ultimate ability to regenerate viable plants. Therefore studies on meristem formation and maintenance are crucial for improving in vitro techniques. Given the economic importance of ornamental plants, it surprising that very few species are commercially mass propagated via somatic embryogenesis. This limitation is mainly due to the lack of optimization of protocols and/or specific culture conditions. This review examines the physiological and molecular events occurring during shoot apical meristem (SAM) formation in vivo and outlines differences in the ontogeny of the SAM produced in vivo and in vitro. Evidence is also provided that the genetic network regulating the function of the SAM in vivo might also operate in culture during the formation of embryogenic and/or organogenic cells. Recent experiments reveal that altered expression of SAM marker genes affects the organogenic and somatic embryogenic processes in vitro with the potential to improve tissue culture in ornamental species.